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- PDB-5dx8: Crystal structure of CARM1, sinefungin, and methylated PABP1 pept... -

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Basic information

Entry
Database: PDB / ID: 5dx8
TitleCrystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R455)
Components
  • Histone-arginine methyltransferase CARM1
  • methylated PABP1 peptide
KeywordsTRANSFERASE / protein-substrate ternary complex
Function / homology
Function and homology information


gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / histone H3R17 methyltransferase activity / glutathione catabolic process / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity ...gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / histone H3R17 methyltransferase activity / glutathione catabolic process / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / glutathione biosynthetic process / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / protein-arginine N-methyltransferase activity / replication fork reversal / positive regulation of epithelial cell apoptotic process / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / positive regulation of fat cell differentiation / response to cAMP / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / Heme signaling / lysine-acetylated histone binding / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / RMTs methylate histone arginines / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / methylation / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Gamma-glutamyltranspeptidase, small subunit / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 ...Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Gamma-glutamyltranspeptidase, small subunit / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Nucleophile aminohydrolases, N-terminal / Vaccinia Virus protein VP39 / Distorted Sandwich / Prokaryotic membrane lipoprotein lipid attachment site profile. / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / Glutathione hydrolase proenzyme / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 Å
AuthorsBoriack-Sjodin, P.A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structural Insights into Ternary Complex Formation of Human CARM1 with Various Substrates.
Authors: Boriack-Sjodin, P.A. / Jin, L. / Jacques, S.L. / Drew, A. / Sneeringer, C. / Scott, M.P. / Moyer, M.P. / Ribich, S. / Moradei, O. / Copeland, R.A.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
E: methylated PABP1 peptide
F: methylated PABP1 peptide
G: methylated PABP1 peptide
H: methylated PABP1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,76712
Polymers166,2428
Non-polymers1,5264
Water6,287349
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
E: methylated PABP1 peptide
F: methylated PABP1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8846
Polymers83,1214
Non-polymers7632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-43 kcal/mol
Surface area26810 Å2
MethodPISA
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
G: methylated PABP1 peptide
H: methylated PABP1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8846
Polymers83,1214
Non-polymers7632
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-41 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.862, 98.266, 207.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4


Mass: 39623.121 Da / Num. of mol.: 4 / Fragment: catalytic domain (UNP residues 134-479)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Plasmid: pFastBac / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q86X55, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Protein/peptide
methylated PABP1 peptide / Poly(A)-binding protein 1


Mass: 1937.315 Da / Num. of mol.: 4 / Fragment: UNP residues 449-466
Mutation: Nterminal biotin and aminohexanoic acid, methylated R455 and R460
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P11940
#3: Chemical
ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe N-terminal of PABP1 peptide is modified with biotin and aminohexanoic acid.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 103564 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.5
Reflection shellResolution: 1.94→2.06 Å / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.6 / % possible all: 92.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.215 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 5156 5 %RANDOM
Rwork0.2038 ---
obs0.2059 97410 90.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.65 Å2 / Biso mean: 26.083 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-0 Å2
2--0.3 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: final / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11274 0 108 349 11731
Biso mean--21.03 28.65 -
Num. residues----1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911864
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211150
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.95816117
X-RAY DIFFRACTIONr_angle_other_deg0.786325648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29951451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30423.971554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95151956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4131558
X-RAY DIFFRACTIONr_chiral_restr0.080.21766
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022916
X-RAY DIFFRACTIONr_mcbond_it1.4442.4715703
X-RAY DIFFRACTIONr_mcbond_other1.4432.4715703
X-RAY DIFFRACTIONr_mcangle_it2.243.6947127
LS refinement shellResolution: 1.941→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 374 -
Rwork0.309 6908 -
all-7282 -
obs--87.28 %

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